Gbrowser

dreg_djangoapp/output_views.py

@@ -1,4 +1,11 @@
 from django.template.loader import render_to_string
+from airavata.model.application.io.ttypes import DataType
+from airavata.model.data.replica.ttypes import (
+    ReplicaLocationCategory,
+)
+from django.conf import settings
+from urllib.parse import urlparse, urlencode
+import base64
 
 
 class DregGenomeBrowserViewProvider:
@@ -9,7 +16,50 @@ class DregGenomeBrowserViewProvider:
     # fixture_output_file = ""
 
     def generate_data(self, request, experiment_output, experiment, output_file=None):
+        #Changing test experiment as all files are not present in the provided experiment
+        #experiment =  request.airavata_client.getExperiment(request.authz_token, 'Clone_of_dREG_peak_calling_on_Aug_9,_2019_10:30_AM_2a27c8d8-6985-4795-9bd3-f6d28619c57f')
+
+        exp_data_dir = experiment.userConfigurationData.experimentDataDir
+        data_root = settings.GATEWAY_DATA_STORE_DIR
+        #data_root = "/var/www/portals/gateway-user-data/cornelldna/"
+
+        #remove data root from the path so that gbfile and gbrowser views can
+        #read the data root from settings
+        if exp_data_dir.startswith(data_root):
+            exp_data_dir = exp_data_dir.replace(data_root, "", 1)
+
+        param_prefix = "out"
+
+        filelist = ''
+        if ( len(experiment.experimentInputs) > 0):
+            for input in experiment.experimentInputs:
+                if(input.type == DataType.URI):
+                    data_product_model = request.airavata_client.getDataProduct(
+                                    request.authz_token, input.value)
+                    for rp in data_product_model.replicaLocations:
+                        if rp.replicaLocationCategory == ReplicaLocationCategory.GATEWAY_DATA_STORE:
+                            current_ouput_path = rp.filePath
+                            path = urlparse(current_ouput_path).path.replace(data_root+exp_data_dir,"",1).replace('/',"",1)
+                            break
+
+                    filelist = filelist + path + "\n"
+                else:
+                    filelist = filelist + input.value + "\n"
+
+        filelist = exp_data_dir + "/\n" + filelist
+        filelist = filelist + param_prefix + "\n";
+
+        encoded_filelist = base64.b64encode(bytes(filelist, 'utf-8')).decode('utf-8')
+
+        #build url
+        http_protocol = request.scheme
+
+        gbURL = "http://epigenomegateway.wustl.edu/browser/?datahub=" + \
+                        http_protocol + "://" + request.META['HTTP_HOST'] +\
+                        "/dreg/gbrowser/" + encoded_filelist + "&genome="
+        js = 'alert("Js is executed")';
         return {
             'output': render_to_string(
-                'dreg_djangoapp/dreg_genome_browser.html')
-        }
+                'dreg_djangoapp/dreg_genome_browser.html', {'gbURL' : gbURL}),
+            'js': "/static/dreg/gbrowser.js"
+            }

dreg_djangoapp/static/dreg/gbrowser.js

@@ -0,0 +1,7 @@
+$('#gbLinks').on('click', function(e) {
+    gb = $('#genomebuilder').val();
+    var gbUrl = e.target.getAttribute('data-url');
+    console.log(gbUrl + gb)
+    window.open(gbUrl + gb);
+    return false;
+});

dreg_djangoapp/templates/dreg_djangoapp/dreg_genome_browser.html

@@ -8,7 +8,7 @@
   or input
   <input type="text" id="customeGB" style="width:40px" />
   <button
-    id="gbLinks"
+    id="gbLinks" data-url ={{ gbURL }}
     style="color: #fff; background-color: #3e5a43; border-color: #46b8da; border: 1px solid transparent;"
   >
     Switch to genome browser&nbsp;<span

dreg_djangoapp/urls.py

@@ -5,4 +5,6 @@
 app_name = 'dreg_djangoapp'
 urlpatterns = [
     url(r'^hello/', views.hello_world, name="hello"),
+    url(r'^gbrowser/(?P<filelist>[^/]+)/$', views.gbrowser_dreg, name = 'gbrowser_dreg'),
+    url(r'^gbfile/', views.gbfile_download, name = 'gbfile_download')
 ]

dreg_djangoapp/views.py

@@ -1,5 +1,100 @@
+import base64
+import os
+import json
+import re
+
 from django.shortcuts import render
+from django.http import Http404, HttpResponse
+from django.conf import settings
 
 # Create your views here.
 def hello_world(request):
     return render(request, "dynamic_djangoapp/hello.html")
+
+
+def gbrowser_dreg(request, filelist):
+    print("Dreg view is called....")
+
+    #Check if the list of file is included in the request
+    if filelist:
+        #filelist = request.GET['filelist']
+        data_root = settings.GATEWAY_DATA_STORE_DIR
+        #data_root = "/var/www/portals/gateway-user-data/cornelldna/"
+        http_protocol = request.scheme
+        text_format = 'utf-8'
+        json_data = []
+        content = {}
+
+        decoded_filelist = base64.b64decode(filelist).decode(text_format).split("\n")
+        out_prefix = decoded_filelist[3]
+        filelist_encoded = list()
+        print(decoded_filelist)
+        # input file 1
+        content['type']= "bigwig"
+        encoded_file = base64.b64encode(bytes(decoded_filelist[0] + decoded_filelist[1], text_format)).decode(text_format)
+        content['url'] =  http_protocol + '://' + request.META['HTTP_HOST'] + '/dreg/gbfile/?file=' + encoded_file
+        content['name'] = decoded_filelist[1]
+        content['summarymethod'] = "max"
+        content['colorpositive'] = "#C5000B"
+        content['colornegative'] = "#0084D1"
+        content['height'] = 100
+        content['mode'] = "show"
+        json_data.append(dict(content))
+
+        # input file 2
+        encoded_file = base64.b64encode(bytes(decoded_filelist[0] + decoded_filelist[2], text_format)).decode(text_format)
+        content['url'] = http_protocol + '://' + request.META['HTTP_HOST'] + '/dreg/gbfile/?file=' + encoded_file
+        content['name'] = decoded_filelist[2]
+        json_data.append(dict(content))
+
+        # out file 1
+        encoded_file = base64.b64encode(bytes(decoded_filelist[0]+'ARCHIVE/out.dREG.infp.bw', text_format)).decode(text_format)
+        content['url'] = http_protocol + '://' + request.META['HTTP_HOST'] + '/dreg/gbfile/?file=' + encoded_file
+        content['name'] = "dREG Info. Sites:"
+        content['mode'] = "show"
+        content['colorpositive'] = "#B30086"
+        content['colornegative'] = "#0000e5"
+        content['backgroundcolor'] = "#ffffe5"
+        content["height"] =  40
+        content['fixedscale'] = dict({'min':0, 'max':1})
+        json_data.append(dict(content))
+
+        # out file 2
+        encoded_file = base64.b64encode(bytes(decoded_filelist[0]+'ARCHIVE/out.dREG.peak.score.bw', text_format)).decode(text_format)
+        content['url'] = http_protocol + '://' + request.META['HTTP_HOST'] + '/dreg/gbfile/?file=' + encoded_file
+        content['name'] = "dREG Peak Calling:"
+        content['mode'] = "show"
+        content['colorpositive'] = "#B30086"
+        content['colornegative'] = "#0000e5"
+        content['backgroundcolor'] = "#ffffe5"
+        content["height"] =  40
+        content['fixedscale'] = dict({'min':0.2, 'max':1.0})
+        json_data.append(dict(content))
+        print(json_data)
+
+        dump = json.dumps(json_data)
+        dump_cleaned = re.sub(r'"(\w*?)": ', r'\1:', dump)
+        #print(dump)
+    return HttpResponse(dump_cleaned, content_type='text/plain')
+
+
+def gbfile_download(request):
+    #TODO: decode filenames and path from the url text
+    text_format = 'utf-8'
+    file_path = ""
+    if 'file' in request.GET:
+        file = request.GET['file']
+        decoded_filepath = base64.b64decode(file).decode(text_format)
+        filename = os.path.basename(decoded_filepath)
+        data_root = settings.GATEWAY_DATA_STORE_DIR
+        # Change this to test it locally
+        #data_root = "/var/www/portals/gateway-user-data/cornelldna/"
+        #data_root = settings.MEDIA_ROOT + '/dreg/'
+        file_path = os.path.join(data_root, decoded_filepath.lstrip("/"))
+
+    if os.path.exists(file_path):
+        with open(file_path, 'rb') as fh:
+            response = HttpResponse(fh.read(), content_type="application/octet-stream")
+            response['Content-Disposition'] = 'attachment; filename=' + os.path.basename(file_path)
+            return response
+    raise Http404